51
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Sandler I, Chen J, Taylor M, Sharma S, Ho J. Accuracy of DLPNO-CCSD(T): Effect of Basis Set and System Size. J Phys Chem A 2021; 125:1553-1563. [PMID: 33560853 DOI: 10.1021/acs.jpca.0c11270] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The DLPNO-CCSD(T) method is designed to study large molecular systems at significantly reduced cost relative to its canonical counterpart. However, the error in this approach is also size-extensive and relies on cancellation of errors for the calculation of relative energies. This work provides a direct comparison of canonical CCSD(T) and TightPNO DLPNO-CCSD(T) calculations of reaction energies and barriers of a broad range of chemical reactions. The dataset includes acidities, anion binding affinities, enolization, Diels-Alder, nucleophilic substitution, and atom transfer reactions and complements existing theoretical datasets in terms of system size as well as new reaction types (e.g., anion binding affinities and chlorine atom transfer reactions). The performance of DLPNO-CCSD(T) was further examined with respect to systematic variation of basis set and system size and amounts of nonbonded interaction present in the system. The errors in the DLPNO-CCSD(T) were found to be relatively insensitive to the choice of basis set for small systems but increase monotonically with system size. Additionally, calculations of barriers appear to be more challenging than reaction energies with errors exceeding 5 kJ mol-1 for many Diels-Alder reactions. Further tests on three realistic organic reactions reveal the impact of the DLPNO approximation in calculating absolute and relative barriers that are important for predictions such as stereoselectivity.
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Affiliation(s)
- Isolde Sandler
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Junbo Chen
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Mackenzie Taylor
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Shaleen Sharma
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Junming Ho
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
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52
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Zhu Q, Gu Y, Hu L, Gaudin T, Fan M, Ma J. Shear viscosity prediction of alcohols, hydrocarbons, halogenated, carbonyl, nitrogen-containing, and sulfur compounds using the variable force fields. J Chem Phys 2021; 154:074502. [PMID: 33607909 DOI: 10.1063/5.0038267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Viscosity of organic liquids is an important physical property in applications of printing, pharmaceuticals, oil extracting, engineering, and chemical processes. Experimental measurement is a direct but time-consuming process. Accurately predicting the viscosity with a broad range of chemical diversity is still a great challenge. In this work, a protocol named Variable Force Field (VaFF) was implemented to efficiently vary the force field parameters, especially λvdW, for the van der Waals term for the shear viscosity prediction of 75 organic liquid molecules with viscosity ranging from -9 to 0 in their nature logarithm and containing diverse chemical functional groups, such as alcoholic hydroxyl, carbonyl, and halogenated groups. Feature learning was applied for the viscosity prediction, and the selected features indicated that the hydrogen bonding interactions and the number of atoms and rings play important roles in the property of viscosity. The shear viscosity prediction of alcohols is very difficult owing to the existence of relative strong intermolecular hydrogen bonding interaction as reflected by density functional theory binding energies. From radial and spatial distribution functions of methanol, we found that the van der Waals related parameters λvdW are more crucial to the viscosity prediction than the rotation related parameters, λtor. With the variable λvdW-based all-atom optimized potentials for liquid simulations force field, a great improvement was observed in the viscosity prediction for alcohols. The simplicity and uniformity of VaFF make it an efficient tool for the prediction of viscosity and other related properties in the rational design of materials with the specific properties.
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Affiliation(s)
- Qiang Zhu
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education Institute of Theoretical and Computational Chemistry School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Yuming Gu
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education Institute of Theoretical and Computational Chemistry School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Limu Hu
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education Institute of Theoretical and Computational Chemistry School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Théophile Gaudin
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education Institute of Theoretical and Computational Chemistry School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Mengting Fan
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education Institute of Theoretical and Computational Chemistry School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jing Ma
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education Institute of Theoretical and Computational Chemistry School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
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53
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Paz ASP, Glover WJ. Diabatic Many-Body Expansion: Development and Application to Charge-Transfer Reactions. J Chem Theory Comput 2021; 17:1497-1511. [DOI: 10.1021/acs.jctc.0c01231] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amiel S. P. Paz
- NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshang Road North, Shanghai 200062, China
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - William J. Glover
- NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshang Road North, Shanghai 200062, China
- Department of Chemistry, New York University, New York, New York 10003, United States
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54
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Fu F, Liao K, Liu Z, Hong D, Yang H, Tian Y, Wei W, Liu C, Li S, Ma J, Li W. Controlled Fluorescence Enhancement of DNA-Binding Dye Through Chain Length Match between Oligoguanine and TOTO. J Phys Chem B 2021; 125:518-527. [PMID: 33426891 DOI: 10.1021/acs.jpcb.0c09611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Fluorescent DNA-binding dyes are extensively employed as probe and biosensing in biological detection and imaging. Experiments and theoretical calculations of thiazole orange homodimeric (TOTO) dye binding to a single-strand DNA (ssDNA), poly(dG)n (n = 2, 4, 6, 8), reveal that the n = 6 complex shows about 300-fold stronger fluorescence than n = 2, 4 and a slightly stronger one than n = 8 complexes, which is benefited from the length match between TOTO and poly(dG)6. The machine learning, based on molecular dynamics trajectories, indicates that TOTO is featured by the dihedral angle along its backbone and its end-to-end distance, in which the latter one defines the stretch and hairpin structures of TOTO, respectively. The time-dependent density functional theory calculations on the low-lying excited states show that the stretched TOTO with π-π end-stacking binding mode can bring about strong fluorescence with localized π-π* transitions. For the n = 2, 4, and 8 complexes, the linear scaling quantum mechanics calculations indicate that the dominant hairpin TOTO with intercalative binding modes have relatively larger binding energies, leading to fluorescence quenching by intramolecular charge transfer. Our results may provide an insight for modulating the DNA-dye binding modes to tune the degree of charge transfer and designing fluorescent probes for the recognition of specific DNA sequences.
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Affiliation(s)
- Fangjia Fu
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Kang Liao
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Ziteng Liu
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Daocheng Hong
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Haitang Yang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Yuxi Tian
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Wei Wei
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Chungen Liu
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Jing Ma
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
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55
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Li W, Dong H, Ma J, Li S. Structures and Spectroscopic Properties of Large Molecules and Condensed-Phase Systems Predicted by Generalized Energy-Based Fragmentation Approach. Acc Chem Res 2021; 54:169-181. [PMID: 33350806 DOI: 10.1021/acs.accounts.0c00580] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
ConspectusThe structures and spectroscopic properties of molecules and condensed-phase systems are usually experimentally characterized by X-ray, infrared (IR), Raman, nuclear magnetic resonance (NMR), and electronic absorption/emission spectra. Quantum mechanics (QM) calculations are critical in quantitatively understanding the relationship between the structure and physicochemical properties of various chemical systems. However, it is very challenging to apply traditional QM methods to large molecules and condensed-phase systems with large unit cells due to their steep computational scaling with the system size. To overcome this difficulty, theoretical chemists have developed various linear (or low) scaling QM methods, among which energy-based fragmentation methods have achieved great success for large molecules or clusters. One of the most popular energy-based fragmentation methods is the generalized energy-based fragmentation (GEBF) approach developed by us.In this approach, the ground-state energy of a large molecule can be evaluated from the ground-state energies of a series of embedded subsystems. In this Account, we focus on the recent developments and applicability of the GEBF approach for the structures and spectroscopic properties of complicated large molecules and condensed-phase systems. With new fragmentation schemes, the GEBF approach can now describe ionic liquid clusters and metal-containing supramolecular systems accurately and can provide accurate binding energies for host-guest complexes. In addition, the GEBF approach is now available for describing the localized excited states of large systems including a chromophore. More importantly, the GEBF approach under periodic boundary conditions (PBC-GEBF) has been developed to deal with periodic molecular crystals and liquids. Then, the ground-state energy (or property) per unit cell of a periodic condensed phase system can be predicted with QM calculations on nonperiodic embedded subsystems. This feature enables accurate electron correlation calculations on molecular crystals and liquids to be feasible on ordinary workstations. The PBC-GEBF approach has been applied to predict the crystal structures, lattice energies, and spectroscopic properties of some typical molecular crystals and solutions. By combining the GEBF method and machine learning (ML) method, a GEBF-ML force field has been developed for long normal alkanes, and the IR spectra of long alkanes can be obtained from the GEBF-ML molecular dynamics (MD) simulations. The GEBF and its periodic variant are expected to play increasingly important roles in investigating real-life chemical systems of broad interests at the ab initio levels.
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Affiliation(s)
- Wei Li
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Hao Dong
- Kuang Yaming Honors School and Institute for Brain Sciences, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Jing Ma
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Shuhua Li
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
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56
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Ricard TC, Iyengar SS. Efficient and Accurate Approach To Estimate Hybrid Functional and Large Basis-Set Contributions to Condensed-Phase Systems and Molecule–Surface Interactions. J Chem Theory Comput 2020; 16:4790-4812. [DOI: 10.1021/acs.jctc.9b01089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Timothy C. Ricard
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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57
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Cheng Z, Zhao D, Ma J, Li W, Li S. An On-the-Fly Approach to Construct Generalized Energy-Based Fragmentation Machine Learning Force Fields of Complex Systems. J Phys Chem A 2020; 124:5007-5014. [DOI: 10.1021/acs.jpca.0c04526] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Zheng Cheng
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Dongbo Zhao
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Jing Ma
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Wei Li
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Shuhua Li
- Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
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58
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Liu J, He X. Fragment-based quantum mechanical approach to biomolecules, molecular clusters, molecular crystals and liquids. Phys Chem Chem Phys 2020; 22:12341-12367. [PMID: 32459230 DOI: 10.1039/d0cp01095b] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
To study large molecular systems beyond the system size that the current state-of-the-art ab initio electronic structure methods could handle, fragment-based quantum mechanical (QM) approaches have been developed over the past years, and proved to be efficient in dealing with large molecular systems at various ab initio levels. According to the fragmentation approach, a large molecular system can be divided into subsystems (fragments), and subsequently the property of the whole system can be approximately obtained by taking a proper combination of the corresponding terms of individual fragments. Therefore, the standard QM calculation of a large system could be circumvented by carrying out a series of calculations on small fragments, which significantly promotes computational efficiency. The electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method is one of the fragment-based QM approaches which has been developed by our research group in recent years. This Perspective presents the theoretical framework of this fragmentation method and its applications in biomolecules, molecular clusters, molecular crystals and liquids, including total energy calculation, protein-ligand/protein binding affinity prediction, geometry optimization, vibrational spectrum simulation, ab initio molecular dynamics simulation, and prediction of excited-state properties.
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Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
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59
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Chen X, Gao J. Fragment Exchange Potential for Realizing Pauli Deformation of Interfragment Interactions. J Phys Chem Lett 2020; 11:4008-4016. [PMID: 32308000 DOI: 10.1021/acs.jpclett.0c00933] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In fragment-based methods, the lack of explicit short-range exchange interactions between monomers can result in unphysical deformation in charge density. In this study, we describe a fragment exchange potential (XFP) to explicitly account for interfragmental Pauli deformation. In our implementation, a Kohn-Sham exchange potential is adopted along with the Yukawa potential. The method has been validated by comparison of the computed exchange energies using the XFP potential with results obtained from antisymmetrized fragmental orbitals on the S66×8 data set containing 528 bimolecular interactions of equilibrium and arbitrary geometries. It was also found that it is only necessary to deploy numerical grids on atoms within their van der Waals contacts, significantly reducing the small, albeit extra, computational cost. We anticipate that the XFP presented here may be applied to molecular dynamics simulations of macromolecules using a fragment-based quantum mechanical potential with improved SCF convergence and computational accuracy.
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Affiliation(s)
- Xin Chen
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, P. R. China
| | - Jiali Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
- Department of Chemistry and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
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60
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Zhao D, Shen X, Cheng Z, Li W, Dong H, Li S. Accurate and Efficient Prediction of NMR Parameters of Condensed-Phase Systems with the Generalized Energy-Based Fragmentation Method. J Chem Theory Comput 2020; 16:2995-3005. [DOI: 10.1021/acs.jctc.9b01298] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Dongbo Zhao
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People’s Republic of China
- Kuang Yaming Honors School, Nanjing University, 210023 Nanjing, People’s Republic of China
| | - Xiaoling Shen
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People’s Republic of China
| | - Zheng Cheng
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People’s Republic of China
| | - Wei Li
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People’s Republic of China
| | - Hao Dong
- Kuang Yaming Honors School, Nanjing University, 210023 Nanjing, People’s Republic of China
- Institute for Brain Sciences, Nanjing University, 210023 Nanjing, People’s Republic of China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People’s Republic of China
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61
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Dawson W, Mohr S, Ratcliff LE, Nakajima T, Genovese L. Complexity Reduction in Density Functional Theory Calculations of Large Systems: System Partitioning and Fragment Embedding. J Chem Theory Comput 2020; 16:2952-2964. [PMID: 32216343 DOI: 10.1021/acs.jctc.9b01152] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
With the development of low order scaling methods for performing Kohn-Sham density functional theory, it is now possible to perform fully quantum mechanical calculations of systems containing tens of thousands of atoms. However, with an increase in the size of the system treated comes an increase in complexity, making it challenging to analyze such large systems and determine the cause of emergent properties. To address this issue, in this paper, we present a systematic complexity reduction methodology which can break down large systems into their constituent fragments and quantify interfragment interactions. The methodology proposed here requires no a priori information or user interaction, allowing a single workflow to be automatically applied to any system of interest. We apply this approach to a variety of different systems and show how it allows for the derivation of new system descriptors, the design of QM/MM partitioning schemes, and the novel application of graph metrics to molecules and materials.
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Affiliation(s)
- William Dawson
- RIKEN Center for Computational Science, Kobe 650-0047, Japan
| | - Stephan Mohr
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Laura E Ratcliff
- Department of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Luigi Genovese
- Université Grenoble Alpes, INAC-MEM, L_Sim, Grenoble F-38000, France.,CEA, INAC-MEM, L_Sim, Grenoble F-38000, France
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62
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QM Implementation in Drug Design: Does It Really Help? Methods Mol Biol 2020. [PMID: 32016884 DOI: 10.1007/978-1-0716-0282-9_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Abstract
Computational chemistry allows one to characterize the structure, dynamics, and energetics of protein-ligand interactions, which makes it a valuable tool in drug discovery in both academic research and pharmaceutical industry. Molecular mechanics (MM)-based approaches are widely utilized to assist the discovery of new drug candidates. However, the complexity of protein-ligand interactions challenges the accuracy and efficiency of the commonly used empirical methods. Aiming to provide better accuracy in the description of protein-ligand interactions, quantum mechanics (QM)-based approaches are becoming increasingly explored. In principle, QM calculation includes all contributions to the energy, accounting for terms usually missing in empirical force fields, and provides a greater degree of transferability. The usefulness of QM in drug design cannot be overemphasized. In this chapter, we present recent developments and applications of fragment-based QM method in studying the protein-ligand and protein-protein interactions. We critically discuss the performance of the fragment-based QM method at different ab initio levels while trying to answer a critical question: do QM-based methods really help in drug design?
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63
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Tóth Z, Kubečka J, Muchová E, Slavíček P. Ionization energies in solution with the QM:QM approach. Phys Chem Chem Phys 2020; 22:10550-10560. [PMID: 32010902 DOI: 10.1039/c9cp06154a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We discuss a fragment-based QM:QM scheme as a practical way to access the energetics of vertical electronic processes in the condensed phase. In the QM:QM scheme, we decompose the large molecular system into small fragments, which interact solely electrostatically. The energies of the fragments are calculated in a self-consistent field generated by the other fragments and the total energy of the system is calculated as a sum of the fragment energies. We show on two test cases (cytosine and a sodium cation) that the method allows one to accurately simulate the shift of vertical ionization energies (VIE) while going from the gas phase to the bulk. For both examples, the predicted solvent shifts and peak widths estimated at the DFT level agree well with the experimental observations. We argue that the QM:QM approach is more suitable than either an electrostatic embedding based QM/MM approach, a full quantum description at the DFT level with a generally used functional or a combination of both. We also discuss the potential scope of the applicability for other electronic processes such as Auger decay.
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Affiliation(s)
- Zsuzsanna Tóth
- University of Chemistry and Technology Prague, Department of Physical Chemistry, Technická 5, 16628 Prague 6, Czech Republic.
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64
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Abstract
Since the introduction of the fragment molecular orbital method 20 years ago, fragment-based approaches have occupied a small but growing niche in quantum chemistry. These methods decompose a large molecular system into subsystems small enough to be amenable to electronic structure calculations, following which the subsystem information is reassembled in order to approximate an otherwise intractable supersystem calculation. Fragmentation sidesteps the steep rise (with respect to system size) in the cost of ab initio calculations, replacing it with a distributed cost across numerous computer processors. Such methods are attractive, in part, because they are easily parallelizable and therefore readily amenable to exascale computing. As such, there has been hope that distributed computing might offer the proverbial "free lunch" in quantum chemistry, with the entrée being high-level calculations on very large systems. While fragment-based quantum chemistry can count many success stories, there also exists a seedy underbelly of rarely acknowledged problems. As these methods begin to mature, it is time to have a serious conversation about what they can and cannot be expected to accomplish in the near future. Both successes and challenges are highlighted in this Perspective.
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Affiliation(s)
- John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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65
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Kumar A, Iyengar SS. Fragment-Based Electronic Structure for Potential Energy Surfaces Using a Superposition of Fragmentation Topologies. J Chem Theory Comput 2019; 15:5769-5786. [DOI: 10.1021/acs.jctc.9b00608] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Anup Kumar
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana-47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana-47405, United States
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66
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Nandi A, Qu C, Bowman JM. Full and fragmented permutationally invariant polynomial potential energy surfaces for trans and cis N-methyl acetamide and isomerization saddle points. J Chem Phys 2019; 151:084306. [DOI: 10.1063/1.5119348] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Apurba Nandi
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Chen Qu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | - Joel M. Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
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67
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Liu J, Rana B, Liu KY, Herbert JM. Variational Formulation of the Generalized Many-Body Expansion with Self-Consistent Charge Embedding: Simple and Correct Analytic Energy Gradient for Fragment-Based ab Initio Molecular Dynamics. J Phys Chem Lett 2019; 10:3877-3886. [PMID: 31251619 DOI: 10.1021/acs.jpclett.9b01214] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The many-body expansion (MBE) and its extension to overlapping fragments, the generalized (G)MBE, constitute the theoretical basis for most fragment-based approaches for large-scale quantum chemistry. We reformulate the GMBE for use with embedding charges determined self-consistently from the fragment wave functions, in a manner that preserves the variational nature of the underlying self-consistent field method. As a result, the analytic gradient retains the simple "sum of fragment gradients" form that is often assumed in practice, sometimes incorrectly. This obviates (without approximation) the need to solve coupled-perturbed equations, and we demonstrate stable, fragment-based ab initio molecular dynamics simulations using this technique. Energy conservation fails when charge-response contributions to the Fock matrix are neglected, even while geometry optimizations and vibrational frequency calculations may yet be accurate. Stable simulations can be recovered by means of straightforward modifications introduced here, providing a general paradigm for fragment-based ab initio molecular dynamics.
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Affiliation(s)
- Jie Liu
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Bhaskar Rana
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Kuan-Yu Liu
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - John M Herbert
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
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68
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Liu J, Sun H, Glover WJ, He X. Prediction of Excited-State Properties of Oligoacene Crystals Using Fragment-Based Quantum Mechanical Method. J Phys Chem A 2019; 123:5407-5417. [PMID: 31187994 DOI: 10.1021/acs.jpca.8b12552] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A fundamental understanding of the excited-state properties of molecular crystals is of central importance for their optoelectronics applications. In this study, we developed the electrostatically embedded generalized molecular fractionation (EE-GMF) method for the quantitative characterization of the excited-state properties of locally excited molecular clusters. The accuracy of the EE-GMF method is systematically assessed for oligoacene crystals. Our result demonstrates that the EE-GMF method is capable of providing the lowest vertical singlet (S1) and triplet excitation energies (T1), in excellent agreement with the full-system quantum mechanical calculations. Using this method, we also investigated the performance of different density functionals in predicting the excited-state properties of the oligoacene crystals. Among the 13 tested functionals, B3LYP and MN15 give the two lowest overall mean unsigned errors with reference to the experimental S1 and T1 excitation energies. The EE-GMF approach can be readily utilized for studying the excited-state properties of large-scale organic solids at diverse ab initio levels.
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Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy , China Pharmaceutical University , Nanjing 210009 , China
| | | | - William J Glover
- NYU Shanghai , Shanghai 200122 , China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062 , China.,Department of Chemistry , New York University , New York , New York 10003 , United States
| | - Xiao He
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062 , China
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69
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Qu C, Bowman JM. A fragmented, permutationally invariant polynomial approach for potential energy surfaces of large molecules: Application to N-methyl acetamide. J Chem Phys 2019; 150:141101. [PMID: 30981221 DOI: 10.1063/1.5092794] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We describe and apply a method to extend permutationally invariant polynomial (PIP) potential energy surface (PES) fitting to molecules with more than 10 atoms. The method creates a compact basis of PIPs as the union of PIPs obtained from fragments of the molecule. An application is reported for trans-N-methyl acetamide, where B3LYP/cc-pVDZ electronic energies and gradients are used to develop a full-dimensional potential for this prototype peptide molecule. The performance of several fragmented bases is verified against a benchmark PES using all (66) Morse variables. The method appears feasible for much larger molecules.
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Affiliation(s)
- Chen Qu
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Joel M Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
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70
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Chi Y, You X. Kinetics of Hydrogen Abstraction Reactions of Methyl Palmitate and Octadecane by Hydrogen Atoms. J Phys Chem A 2019; 123:3058-3067. [PMID: 30893997 DOI: 10.1021/acs.jpca.8b08802] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogen abstractions play a crucial role in the consumption of fuel molecules during fuel pyrolysis and combustion processes. In this study, a generalized energy-based fragmentation approach was used to obtain CCSD(T)-F12a/cc-pVTZ energy barriers of hydrogen abstraction reactions by hydrogen atoms from methyl palmitate (C15H31COOCH3), a key component of biodiesel. The accuracy of M06-2X/6-311++G(d,p) for obtaining the energy barriers was evaluated against the CCSD(T) results. Based on the quantum chemical results, the high-pressure-limit rate constants for C15H31COOCH3 + H were calculated and compared with those of octadecane ( n-C18H38) reacting with H. The treatment of hindered internal rotations for such long-chain molecules was discussed and the rate rules for different abstraction sites were summarized. The results show that in the C15H31COOCH3 + H system, the α hydrogen abstraction no longer plays a dominant role as in small methyl esters, and the hydrogen atoms of CH2 groups far away from the ester group are more easily abstracted than those near the ester group.
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Affiliation(s)
- Yawei Chi
- Center for Combustion Energy , Tsinghua University , Beijing 100084 , China.,Key Laboratory for Thermal Science and Power Engineering of Ministry of Education , Tsinghua University , Beijing 100084 , China
| | - Xiaoqing You
- Center for Combustion Energy , Tsinghua University , Beijing 100084 , China.,Key Laboratory for Thermal Science and Power Engineering of Ministry of Education , Tsinghua University , Beijing 100084 , China
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71
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Wang F, Zhao D, Jiang L, Song J, Liu Y. THz vibrational spectroscopy for RNA basepair cocrystals and oligonucleotide sequences. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 209:49-54. [PMID: 30343109 DOI: 10.1016/j.saa.2018.10.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/10/2018] [Accepted: 10/13/2018] [Indexed: 05/22/2023]
Abstract
Fourier infrared spectrometer and X-ray diffractometer were used to detect the spectra of lab-made U:A (uracil and adenine hydrate dried at room temperature), lab-made C:G (cytosine and guanine hydrate dried at room temperature), U + A (mixture of uracil and adenine), and C + G (mixture of cytosine and guanine). The results of our testing showed that U:A did not form a eutectic, but C:G did. In order to further characterize the vibrational modes of RNA base pair crystals, the absorption spectra of 1‑methyl‑5‑bromouracil‑9‑methyladenine (abbreviated as 1M5BU:9MA) and 1‑methylcytosine‑9‑ethylguanine (abbreviated as 1MC:9EG) were calculated based on the PBC-GEBF (generalized energy-based fragmentation approach under periodic boundary conditions) method. To further study the effect of substituents on the vibrational mode of the crystal structure, the substituents of 1M5BU:9MA and 1MC:9EG were artificially removed. The results of calculation brought out that methyl and ethyl as substituents have little effect on the vibrational spectrum, but halogen atoms such as Br atom in 1M5BU:9MA has a certain influence on the spectrum. Furthermore, THz (terahertz) spectra of the RNA nucleotide sequence 5'-AUCG-3' was analyzed. In the perspective of the spectra with DNA signatures, their spectra show a great deal of similarity regardless of RNA or DNA, or the base sequence difference. This study will provide a very important information for revealing the role of RNA in the formation of biological macromolecules and its mechanism.
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Affiliation(s)
- Fang Wang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China; School of Electronic and Information Engineering, Sanjiang University, Nanjing 210012, People's Republic of China
| | - Dongbo Zhao
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Ling Jiang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Jun Song
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Yunfei Liu
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China.
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72
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Xu M, He X, Zhu T, Zhang JZH. A Fragment Quantum Mechanical Method for Metalloproteins. J Chem Theory Comput 2019; 15:1430-1439. [PMID: 30620584 DOI: 10.1021/acs.jctc.8b00966] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An accurate energy calculation of metalloprotein is of crucial importance and also a theoretical challenge. In this work, a metal molecular fractionation with conjugate caps (metal-MFCC) approach is developed for efficient linear-scaling quantum calculation of potential energy and atomic forces of metalloprotein. In this approach, the potential energy of a given protein is calculated by a linear combination of potential energies of the neighboring residues, two-body interaction energy between non-neighboring residues that are spatially in close contact and the potential energy of the metal binding group. The calculation of each fragment is embedded in a field of point charges representing the remaining protein environment. Numerical studies were carried out to check the performance of this method, and the calculated potential energies and atomic forces all show excellent agreement with the full system calculations at the M06-2X/6-31G(d) level. By combining the energy calculation with molecular dynamic simulation, we performed an ab initio structural optimization for a zinc finger protein with high efficiency. The present metal-MFCC approach is linear-scaling with a low prefactor and trivially parallelizable. The individual fragment typically contains about 50 atoms, and it is thus possible to be calculated at higher levels of the quantum chemistry method. This fragment method can be routinely applied to perform structural optimization and ab initio molecular dynamic simulation for metalloproteins of any size.
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Affiliation(s)
- Mingyuan Xu
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai , 200062 , China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai , 200062 , China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai , 200062 , China
| | - Tong Zhu
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai , 200062 , China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai , 200062 , China
| | - John Z H Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai , 200062 , China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai , 200062 , China.,Department of Chemistry , New York University , New York 10003 , United States
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73
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Fu F, Liao K, Ma J, Cheng Z, Zheng D, Gao L, Liu C, Li S, Li W. How intermolecular interactions influence electronic absorption spectra: insights from the molecular packing of uracil in condensed phases. Phys Chem Chem Phys 2019; 21:4072-4081. [DOI: 10.1039/c8cp06152a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Intermolecular interactions in terms of molecular packing are crucial for the investigation of the absorption spectra of uracil in different environments.
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Affiliation(s)
- Fangjia Fu
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Kang Liao
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Jing Ma
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Zheng Cheng
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Dong Zheng
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Liuzhou Gao
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Chungen Liu
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Shuhua Li
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Wei Li
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
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74
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Ni Z, Li W, Li S. Fully optimized implementation of the cluster-in-molecule local correlation approach for electron correlation calculations of large systems. J Comput Chem 2018; 40:1130-1140. [DOI: 10.1002/jcc.25730] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/27/2018] [Accepted: 09/27/2018] [Indexed: 01/30/2023]
Affiliation(s)
- Zhigang Ni
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE; Institute of Theoretical and Computational Chemistry, Nanjing University; Nanjing 210023 People's Republic of China
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE; Institute of Theoretical and Computational Chemistry, Nanjing University; Nanjing 210023 People's Republic of China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE; Institute of Theoretical and Computational Chemistry, Nanjing University; Nanjing 210023 People's Republic of China
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75
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Ricard TC, Iyengar SS. Efficiently Capturing Weak Interactions in ab Initio Molecular Dynamics with on-the-Fly Basis Set Extrapolation. J Chem Theory Comput 2018; 14:5535-5552. [DOI: 10.1021/acs.jctc.8b00803] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Timothy C. Ricard
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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76
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Meitei OR, Heßelmann A. Geometry optimizations with the incremental molecular fragmentation method. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1142/s0219633618500372] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Nuclear energy gradients for the incremental molecular fragmentation (IMF) method presented in our previous work [Meitei OR, Heßelmann A, Molecular energies from an incremental fragmentation method, J Chem Phys 144(8):084109, 2016] have been derived. Using the second-order Møller–Plesset perturbation theory method to describe the bonded and nonbonded energy and gradient contributions and the uncorrelated Hartree–Fock method to describe the correction increment, it is shown that the IMF gradient can be easily computed by a sum of the underlying individual derivatives of the energy contributions. The performance of the method has been compared against the supermolecular method by optimizing the structures of a range of polyglycine molecules with up to 36 glycine residues in the chain. It is shown that with a sensible set of parameters used in the fragmentation the supermolecular structures can be fairly well reproduced. In a few cases the optimization with the IMF method leads to structures that differ from the supermolecular ones. It was found, however, that these are more stable geometries also on the supermolecular potential energy surface.
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Affiliation(s)
- Oinam Romesh Meitei
- Department Chemie und Pharmazie, Lehrstuhl für Theoretische Chemie, Friedrich-Alexander Universität Erlangen-Nürnberg, Egerlandstr. 3, D-91058 Erlangen, Germany
| | - Andreas Heßelmann
- Department Chemie und Pharmazie, Lehrstuhl für Theoretische Chemie, Friedrich-Alexander Universität Erlangen-Nürnberg, Egerlandstr. 3, D-91058 Erlangen, Germany
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77
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Wang F, Zhao D, Dong H, Jiang L, Huang L, Liu Y, Li S. THz spectra and corresponding vibrational modes of DNA base pair cocrystals and polynucleotides. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 200:195-201. [PMID: 29689511 DOI: 10.1016/j.saa.2018.04.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/26/2018] [Accepted: 04/12/2018] [Indexed: 05/22/2023]
Abstract
The generalized energy-based fragmentation (GEBF) approach has been applied to study the THz spectra and vibrational modes of base pair cocrystals under periodic boundary conditions (denoted as PBC-GEBF). Results of vibrational mode reveal that hydrogen bonds play a pivotal role in the pairing process of base crystals, where most NH and CH bonds stretch to some extent. We also found that hydrogen bonds of a self-made A:T cocrystal completely break in a transition from liquid to the solid state, while self-made C:G cocrystal is different and easier to form a cocrystal, as confirmed by X-ray diffraction (XRD) and terahertz (THz) spectra. Furthermore, we have studied DNA polynucleotides (in both A and B forms) found that the vibrational modes changed a lot during the process of their forming double strand. Despite the key role played by hydrogen bonds, the key contribution originates from collective motions of the main skeleton. A comparative study of the spectra of some stranded fragments suggests that different sequences or forms have similar spectra in THz band. They distinguish from each other mainly in the low-frequency regions, especially below 1 THz. This study would make great contributions to the molecular dynamics model based DNA long-chain structure simulation in the future study.
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Affiliation(s)
- Fang Wang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China; School of Electronic and Information Engineering, Sanjiang University, Nanjing 210012, People's Republic of China
| | - Dongbo Zhao
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Hao Dong
- Kuang Yaming Honors School, Nanjing University, 210023, People's Republic of China
| | - Ling Jiang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Lin Huang
- Forestry College, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Yunfei Liu
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China.
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
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78
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Xu M, Zhu T, Zhang JZH. A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein. Front Chem 2018; 6:189. [PMID: 29900167 PMCID: PMC5989690 DOI: 10.3389/fchem.2018.00189] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/09/2018] [Indexed: 12/28/2022] Open
Abstract
A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC) method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA)9-NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.
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Affiliation(s)
- Mingyuan Xu
- State Key Lab of Precision Spectroscopy, Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Tong Zhu
- State Key Lab of Precision Spectroscopy, Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.,NYU-ECNU Center for Computational Chemistry at New York University Shanghai, Shanghai, China
| | - John Z H Zhang
- State Key Lab of Precision Spectroscopy, Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.,NYU-ECNU Center for Computational Chemistry at New York University Shanghai, Shanghai, China.,Department of Chemistry, New York University, New York, NY, United States.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, China
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79
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Frederix PWJM, Patmanidis I, Marrink SJ. Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments. Chem Soc Rev 2018; 47:3470-3489. [PMID: 29688238 PMCID: PMC5961611 DOI: 10.1039/c8cs00040a] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Indexed: 01/01/2023]
Abstract
In bionanotechnology, the field of creating functional materials consisting of bio-inspired molecules, the function and shape of a nanostructure only appear through the assembly of many small molecules together. The large number of building blocks required to define a nanostructure combined with the many degrees of freedom in packing small molecules has long precluded molecular simulations, but recent advances in computational hardware as well as software have made classical simulations available to this strongly expanding field. Here, we review the state of the art in simulations of self-assembling bio-inspired supramolecular systems. We will first discuss progress in force fields, simulation protocols and enhanced sampling techniques using recent examples. Secondly, we will focus on efforts to enable the comparison of experimentally accessible observables and computational results. Experimental quantities that can be measured by microscopy, spectroscopy and scattering can be linked to simulation output either directly or indirectly, via quantum mechanical or semi-empirical techniques. Overall, we aim to provide an overview of the various computational approaches to understand not only the molecular architecture of nanostructures, but also the mechanism of their formation.
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Affiliation(s)
- Pim W. J. M. Frederix
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
| | - Ilias Patmanidis
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Groningen , The Netherlands . ;
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80
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Ricard TC, Haycraft C, Iyengar SS. Adaptive, Geometric Networks for Efficient Coarse-Grained Ab Initio Molecular Dynamics with Post-Hartree–Fock Accuracy. J Chem Theory Comput 2018; 14:2852-2866. [DOI: 10.1021/acs.jctc.8b00186] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Timothy C. Ricard
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Cody Haycraft
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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81
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Thapa B, Beckett D, Jovan Jose KV, Raghavachari K. Assessment of Fragmentation Strategies for Large Proteins Using the Multilayer Molecules-in-Molecules Approach. J Chem Theory Comput 2018; 14:1383-1394. [DOI: 10.1021/acs.jctc.7b01198] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Bishnu Thapa
- Department of Chemistry, Indiana University, Bloomington 47405, Indiana, United States
| | - Daniel Beckett
- Department of Chemistry, Indiana University, Bloomington 47405, Indiana, United States
| | - K. V. Jovan Jose
- Department of Chemistry, Indiana University, Bloomington 47405, Indiana, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington 47405, Indiana, United States
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82
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Kobayashi M, Fujimori T, Taketsugu T. Automated error control in divide-and-conquer self-consistent field calculations. J Comput Chem 2018; 39:909-916. [DOI: 10.1002/jcc.25174] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/12/2018] [Accepted: 01/12/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Masato Kobayashi
- Department of Chemistry, Faculty of Science, Hokkaido University; Sapporo 060-0810 Japan
- ESICB, Kyoto University; Kyoto 615-8520 Japan
- PRESTO, Japan Science and Technology Agency; Kawaguchi 332-0012 Japan
| | - Toshikazu Fujimori
- Graduate School of Chemical Sciences and Engineering, Hokkaido University; Sapporo 060-0810 Japan
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University; Sapporo 060-0810 Japan
- ESICB, Kyoto University; Kyoto 615-8520 Japan
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83
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Wang W, Sun X, Qu J, Xie X, Qi ZH, Hong D, Jing S, Zheng D, Tian Y, Ma H, Yu S, Ma J. Aggregation-induced visible light absorption makes reactant 1,2-diisocyanoarenes act as photosensitizers in double radical isocyanide insertions. Phys Chem Chem Phys 2018; 19:31443-31451. [PMID: 29159355 DOI: 10.1039/c7cp05936a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The joint computational and experimental efforts reveal that the organic molecule 1,2-diisocyano-4,5-dimethylbenzene (1) acts as both a reactant and a photosensitizer (PS) in a metal-free reaction with perfluoroalkylhalide (2) to produce 2-perfluoroalkyl quinoxalines (3) under visible light. Both the π-π stacking aggregation in crystals and the solvation in various solvents of PS 1 exhibited visible-light absorption at 466 nm in spite of its smaller coefficient than that of the ultraviolet-light absorption. Such an aggregation-assisted visible-light absorption phenomenon is rationalized by theoretical calculations of the condensed-phase properties with the consideration of the explicit polarization effect from the neighboring molecules. Upon irradiation with different wavelengths, the emission colors changed from navy to bright yellow. Fluorescence lifetime measurements show that the emission of 1 comes from its singlet excited state. The aggregation induced emission when excited at 420 nm has a shorter lifetime (0.45 ns) than that of the emission from isolated molecules (2.71 ns) when excited at 381 nm. It is conceived that the aggregation assisted visible light absorption properties may be general in other photo-reactive molecules, such as 1,4-diisocyano-2,5-dimethylbenzene (4), 1,4-dicyanobenzene (5), and 1,4-diisocyanobenzene (6), which are widely used in many photochemical reactions in the absence of any external photosensitizer.
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Affiliation(s)
- Wenmin Wang
- Key Laboratory of Mesoscopic Chemistry of MOE School of Chemistry & Chemical Engineering, Nanjing University, No. 163 Xianlin Road, Nanjing, 210023, P. R. China.
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84
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Bazargan G, Sohlberg K. Advances in modelling switchable mechanically interlocked molecular architectures. INT REV PHYS CHEM 2018. [DOI: 10.1080/0144235x.2018.1419042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Gloria Bazargan
- Department of Chemistry, Drexel University, Philadelphia, PA, USA
| | - Karl Sohlberg
- Department of Chemistry, Drexel University, Philadelphia, PA, USA
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85
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Yuan D, Li Y, Li W, Li S. Structures and properties of large supramolecular coordination complexes predicted with the generalized energy-based fragmentation method. Phys Chem Chem Phys 2018; 20:28894-28902. [DOI: 10.1039/c8cp05548c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The generalized energy-based fragmentation (GEBF) method has been extended to facilitate ab initio calculations of large supramolecular coordination complexes.
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Affiliation(s)
- Dandan Yuan
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing 210023
| | - Yunzhi Li
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing 210023
| | - Wei Li
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing 210023
| | - Shuhua Li
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing 210023
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86
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DeGregorio N, Iyengar SS. Efficient and Adaptive Methods for Computing Accurate Potential Surfaces for Quantum Nuclear Effects: Applications to Hydrogen-Transfer Reactions. J Chem Theory Comput 2017; 14:30-47. [DOI: 10.1021/acs.jctc.7b00927] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Nicole DeGregorio
- Department of Chemistry and
Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and
Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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87
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Liu KY, Herbert JM. Understanding the many-body expansion for large systems. III. Critical role of four-body terms, counterpoise corrections, and cutoffs. J Chem Phys 2017; 147:161729. [DOI: 10.1063/1.4986110] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Kuan-Yu Liu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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88
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Zhao D, Yang L, Yuan Y, Wang H, Dong H, Li S. Molecular Mechanism of Self-Assembly of Aromatic Oligoamides into Interlocked Double-Helix Foldamers. J Phys Chem B 2017; 121:10064-10072. [PMID: 29019673 DOI: 10.1021/acs.jpcb.7b09067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Foldamer, inspired by the structures and functions of biopolymers, is defined as an artificial molecular architecture that can fold into a three-dimensional structure in solution and has been a growing and active field in supramolecular chemistry. The central issue in foldamer science is to understand how the primary sequence of oligomer folds into conformationally ordered structures as well as how individual subunits self-associate into assembly. For duplex structures, these two issues are always interrelated and inseparable with each other. Although the emergence of new foldamer keeps growing, the detailed mechanism remains elusive. On the basis of an artificially synthesized arylamide oligoamide foldamer with its crystal structure available, we constructed a set of four foldamers with a similar backbone but different substituents and aimed at dissecting the folding and self-association mechanisms of a double-helical foldamer with computations. Using molecular simulations at a microsecond time scale, we observed very consistent processes of the spontaneous self-assembly of two single-helical motifs into an entwined complex. Our results reveal that aggregation of two single-helical motifs driven by extensive π-π interactions is energetically favorable and that this spontaneous self-assembly proceeds through an "unwinding-threading-rewinding" mechanism. The detailed mechanisms about the folding and self-assembly in an aromatic oligoamide foldamer we present here disclose how the sequence is associated with a well-ordered three-dimensional structure at atomic level and therefore may have implications for designing new foldamers with versatile functions.
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Affiliation(s)
| | - Ling Yang
- CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, People's Republic of China
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89
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Zhao D, Song R, Li W, Ma J, Dong H, Li S. Accurate Prediction of NMR Chemical Shifts in Macromolecular and Condensed-Phase Systems with the Generalized Energy-Based Fragmentation Method. J Chem Theory Comput 2017; 13:5231-5239. [DOI: 10.1021/acs.jctc.7b00380] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dongbo Zhao
- Key
Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute
of Theoretical and Computational Chemistry, School of Chemistry and
Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
- Kuang
Yaming Honors School, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Ruiheng Song
- Kuang
Yaming Honors School, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Wei Li
- Key
Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute
of Theoretical and Computational Chemistry, School of Chemistry and
Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Jing Ma
- Key
Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute
of Theoretical and Computational Chemistry, School of Chemistry and
Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Hao Dong
- Kuang
Yaming Honors School, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Shuhua Li
- Key
Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute
of Theoretical and Computational Chemistry, School of Chemistry and
Chemical Engineering, Nanjing University, Nanjing 210023, People’s Republic of China
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90
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Nishimura Y, Nakai H. Parallel implementation of efficient charge-charge interaction evaluation scheme in periodic divide-and-conquer density-functional tight-binding calculations. J Comput Chem 2017; 39:105-116. [DOI: 10.1002/jcc.25086] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/01/2017] [Accepted: 10/02/2017] [Indexed: 01/05/2023]
Affiliation(s)
- Yoshifumi Nishimura
- Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku; Tokyo 169-8555 Japan
| | - Hiromi Nakai
- Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku; Tokyo 169-8555 Japan
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering; Waseda University, 3-4-1 Okubo, Shinjuku-ku; Tokyo 169-8555 Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho; Kawaguchi 332-0012 Japan
- ESICB, Kyoto University, Kyotodaigaku-Katsura; Kyoto 615-8520 Japan
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91
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Zhang L, Li W, Fang T, Li S. Accurate Relative Energies and Binding Energies of Large Ice–Liquid Water Clusters and Periodic Structures. J Phys Chem A 2017; 121:4030-4038. [DOI: 10.1021/acs.jpca.7b03376] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lei Zhang
- Institute of Theoretical
and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry
of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wei Li
- Institute of Theoretical
and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry
of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Tao Fang
- Institute of Theoretical
and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry
of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shuhua Li
- Institute of Theoretical
and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry
of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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92
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Wang F, Zhao D, Dong H, Jiang L, Liu Y, Li S. Terahertz spectra of DNA nucleobase crystals: A joint experimental and computational study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 179:255-260. [PMID: 28273628 DOI: 10.1016/j.saa.2017.02.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 02/15/2017] [Accepted: 02/19/2017] [Indexed: 05/28/2023]
Abstract
Terahertz (THz) spectra of DNA nucleobase crystals were experimentally studied by terahertz time domain spectroscopy (THz-TDS), Fourier transform infrared spectroscopy (FTIR), and computationally studied by the generalized energy-based fragmentation approach under periodic boundary conditions (denoted as PBC-GEBF). We analyzed the vibrational spectra of solid-state DNA nucleobases and assigned the corresponding vibrational modes to the main peaks in the experimental spectra with the PBC-GEBF results. The computational results were verified to be in good accordance with the experimental data. Harmonic vibrational frequency results revealed that all the vibrational modes belong to collective vibrational modes, which involve complicated mixtures of inter- and intramolecular displacements, somewhere in the vicinity of 0.5-9THz.
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Affiliation(s)
- Fang Wang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China; School of Electronic and Information Engineering, Sanjiang University, Nanjing 210012, China
| | - Dongbo Zhao
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hao Dong
- Kuang Yaming Honors School, Nanjing University, 210023, China
| | - Ling Jiang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China
| | - Yunfei Liu
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China.
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
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93
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Yuan D, Li Y, Ni Z, Pulay P, Li W, Li S. Benchmark Relative Energies for Large Water Clusters with the Generalized Energy-Based Fragmentation Method. J Chem Theory Comput 2017; 13:2696-2704. [DOI: 10.1021/acs.jctc.7b00284] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Dandan Yuan
- School
of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic
Chemistry of Ministry of Education, Institute of Theoretical and Computational
Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Yunzhi Li
- School
of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic
Chemistry of Ministry of Education, Institute of Theoretical and Computational
Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Zhigang Ni
- School
of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic
Chemistry of Ministry of Education, Institute of Theoretical and Computational
Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Peter Pulay
- Department
of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Wei Li
- School
of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic
Chemistry of Ministry of Education, Institute of Theoretical and Computational
Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Shuhua Li
- School
of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic
Chemistry of Ministry of Education, Institute of Theoretical and Computational
Chemistry, Nanjing University, Nanjing 210023, P. R. China
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94
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Wang F, Zhao D, Jiang L, Xu L, Sun H, Liu Y. A comparative study on the experimental and calculated results of mid-infrared and Raman vibrational modes of nucleic acid bases. J Mol Graph Model 2017; 74:305-314. [PMID: 28475967 DOI: 10.1016/j.jmgm.2017.04.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 04/14/2017] [Accepted: 04/18/2017] [Indexed: 10/19/2022]
Abstract
The MIR (mid-infrared) and Raman spectra of the nucleic acid base powders were tested by Fourier transform infrared spectroscopy and laser Raman spectroscopy. The vibrational modes of nucleic acid base crystals were simulated by the generalized energy-based fragmentation approach under periodic boundary conditions (hereinafter referred as PBC-GEBF) together with Guassian09 software. Taking into account the intermolecular hydrogen bonds in the unit cell and the weak interactions between the unit cells, the PBC-GEBF method adopted by our group was for the first time used for calculating nucleic acid base crystals in the 400-2000cm-1 band. The theoretical and experimental spectra turn out to be in good agreement with each other. Compared with the calculated results of the nucleic acid base monomer, the calculated results of crystals appear to be in better agreement with the experimental results. Some weak vibration peaks were reproduced by simulation, and the positions of the vibration peaks agree well. By analyzing the vibrational modes, it can be observed that the vibrational modes below 1000 cm-1 are mainly characterized by the collective vibrations involving all the molecules in the unit cell. In addition to intramolecular interactions, weak intermolecular interactions (including Van der Waals force and weak hydrogen bond) and the lattice stacking force also contribute to the overall vibrations. This study is of great importance to the analysis of the stability of RNA/DNA structures and their genetic properties.
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Affiliation(s)
- Fang Wang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China; School of Electronic and Information Engineering, Sanjiang University, Nanjing 210012, China
| | - Dongbo Zhao
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Ling Jiang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China
| | - Li Xu
- Advanced Analysis and Testing Center, Nanjing Forestry University, Nanjing 210037, China
| | - Haijun Sun
- Advanced Analysis and Testing Center, Nanjing Forestry University, Nanjing 210037, China
| | - Yunfei Liu
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China.
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95
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Kjærgaard T. The Laplace transformed divide-expand-consolidate resolution of the identity second-order Møller-Plesset perturbation (DEC-LT-RIMP2) theory method. J Chem Phys 2017; 146:044103. [PMID: 28147513 DOI: 10.1063/1.4973710] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The divide-expand-consolidate resolution of the identity second-order Møller-Plesset perturbation (DEC-RI-MP2) theory method introduced in Baudin et al. [J. Chem. Phys. 144, 054102 (2016)] is significantly improved by introducing the Laplace transform of the orbital energy denominator in order to construct the double amplitudes directly in the local basis. Furthermore, this paper introduces the auxiliary reduction procedure, which reduces the set of the auxiliary functions employed in the individual fragments. The resulting Laplace transformed divide-expand-consolidate resolution of the identity second-order Møller-Plesset perturbation method is applied to the insulin molecule where we obtain a factor 9.5 speedup compared to the DEC-RI-MP2 method.
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Affiliation(s)
- Thomas Kjærgaard
- qLEAP Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
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96
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Chen GD, Weng J, Song G, Li ZH. Generalized Switch Functions in the Multilevel Many-Body Expansion Method and Its Application to Water Clusters. J Chem Theory Comput 2017; 13:2010-2020. [DOI: 10.1021/acs.jctc.7b00144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Guo Dong Chen
- Collaborative Innovation Center of Chemistry for Energy Material, Shanghai Key Laboratory of Molecular Catalysis & Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Jingwei Weng
- Collaborative Innovation Center of Chemistry for Energy Material, Shanghai Key Laboratory of Molecular Catalysis & Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Guoliang Song
- Collaborative Innovation Center of Chemistry for Energy Material, Shanghai Key Laboratory of Molecular Catalysis & Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Zhen Hua Li
- Collaborative Innovation Center of Chemistry for Energy Material, Shanghai Key Laboratory of Molecular Catalysis & Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, China
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97
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Haycraft C, Li J, Iyengar SS. Efficient, “On-the-Fly”, Born–Oppenheimer and Car–Parrinello-type Dynamics with Coupled Cluster Accuracy through Fragment Based Electronic Structure. J Chem Theory Comput 2017; 13:1887-1901. [DOI: 10.1021/acs.jctc.6b01107] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Cody Haycraft
- Department of Chemistry and
Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Junjie Li
- Department of Chemistry and
Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and
Department of Physics, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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98
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Fang T, Li Y, Li S. Generalized energy‐based fragmentation approach for modeling condensed phase systems. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1297] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Tao Fang
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational ChemistryNanjing University Nanjing P. R. China
| | - Yunzhi Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational ChemistryNanjing University Nanjing P. R. China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational ChemistryNanjing University Nanjing P. R. China
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99
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Dissociation in Binary Acid/Base Clusters: An Examination of Inconsistencies Introduced Into the Many-Body Expansion by Naïve Fragmentation Schemes. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/bs.arcc.2017.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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100
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Tao Y, Zou W, Jia J, Li W, Cremer D. Different Ways of Hydrogen Bonding in Water - Why Does Warm Water Freeze Faster than Cold Water? J Chem Theory Comput 2016; 13:55-76. [PMID: 27996255 DOI: 10.1021/acs.jctc.6b00735] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The properties of liquid water are intimately related to the H-bond network among the individual water molecules. Utilizing vibrational spectroscopy and modeling water with DFT-optimized water clusters (6-mers and 50-mers), 16 out of a possible 36 different types of H-bonds are identified and ordered according to their intrinsic strength. The strongest H-bonds are obtained as a result of a concerted push-pull effect of four peripheral water molecules, which polarize the electron density in a way that supports charge transfer and partial covalent character of the targeted H-bond. For water molecules with tetra- and pentacoordinated O atoms, H-bonding is often associated with a geometrically unfavorable positioning of the acceptor lone pair and donor σ*(OH) orbitals so that electrostatic rather than covalent interactions increasingly dominate H-bonding. There is a striking linear dependence between the intrinsic strength of H-bonding as measured by the local H-bond stretching force constant and the delocalization energy associated with charge transfer. Molecular dynamics simulations for 1000-mers reveal that with increasing temperature weak, preferentially electrostatic H-bonds are broken, whereas the number of strong H-bonds increases. An explanation for the question why warm water freezes faster than cold water is given on a molecular basis.
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Affiliation(s)
- Yunwen Tao
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Wenli Zou
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Junteng Jia
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, P. R. China
| | - Wei Li
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, P. R. China
| | - Dieter Cremer
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
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